The Mouse Atlas Project aims to produce a collection of SAGE libraries derived from various mouse tissues representing different developmental stages, ranging from embryonic stem cells to post-natal day 84 [21]; currently the resource contains over 200 different libraries.
We believe that our analysis of RNA-seq data from six mouse tissues represents the first comprehensive characterization of isoform usage in these tissues.
In the mouse, tissues were harvested representing the three VLCAD genotypes (+/+, +/−, and −/−) and were snap-frozen in liquid nitrogen, as previously described.[10] Frozen tissue stored at −70°C was used to assess the tissue distribution of TMEM135 in the heart, skeletal muscles, liver and brain of two-month-old mice.
In addition, analysis of expression data representing 61 mouse tissues [ 23] showed that the only RNase T2 homolog present in the mouse genome was also detected in embryonic samples (not shown).
This number represents approximately two thirds of the miRNAs estimated to be expressed in mouse tissues from information in the miRNA registry (Release 5.0).
To test this hypothesis, we performed E2f4 chromatin immunoprecipitations in seven primary mouse tissues and a mouse cell line using promoter microarrays representing 13,000 regions in the mouse genome (Figure 2B).
The ratio of human DNA over mouse DNA represents the number of human cells in mouse tissues.
Indeed, p62 accumulates in several autophagy-deficient mouse tissues (Zatloukal et al, 2002; Martinet et al, 2013) and represents a reliable marker for tissues with reduced autophagic activity (Waguri & Komatsu, 2009).
Given that exon 8b-containing transcripts are ubiquitously expressed and represent roughly half of total B-raf transcripts in mouse tissues, it is surprising to see no phenotype in Δ8b knockout mice.
These results confirm previous findings on comparing human and mouse tissues based on datasets that were normalized differently and in which tissue samples are represented individually [ 18].
